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| Status |
Public on Dec 20, 2023 |
| Title |
PBS treated hepatocytes, replicate 2 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
cell type: Hepatocytes
strain: C57BL/6
treatment: PBS
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraction by Maxwell® 16 Cell LEV DNA Purification Kit and biisufite conversion by EpiTect Bisulfite Kit, following provider indications. Finally, the promoter region of Arid1b and Shroom1 was amplified by PCR.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following the manufacturer’s recommendations
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Reads quality was controlled with Fastqc v0.11.9 while low-quality reads and adapters were removed using Trim_Galore v0.6.6. with the following parameters: --quality 20, --length 25, --paired, --rrbs
Remaining reads were analyzed using the Bismark read mapper Methylation caller tool v0.23.0
In detail, reads were aligned to both unconverted and converted genomes (GRCm38) using bismark with the --local and –non_directional parameters and the methylation status was obtained using bismark_methylation_extractor script using only the reads mapping to the bottom strand (OB and CTOB)
The methylation calls were processed using the R/Bioconductor package MethylKit v1.16.1
Imported data were filtered to retain only cytosines from CpG context in the amplified windows and normalized using the normalizeCoverage function
The information from the different samples was merged using the unite function considering the positions covered in at least 1 replicate per condition. The methylation percentage at each position was calculated using the percMethylation function.
Assembly: GRCm38
Supplementary files format and content: Bismark coverage
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| Submission date |
Aug 16, 2023 |
| Last update date |
Dec 20, 2023 |
| Contact name |
Sara Valsoni |
| E-mail(s) |
[email protected]
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| Organization name |
SR-TIGET
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| Department |
TIGET
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| Street address |
via Olgettina 60
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| City |
Milano |
| State/province |
MI |
| ZIP/Postal code |
20132 |
| Country |
Italy |
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| Platform ID |
GPL16417 |
| Series (2) |
| GSE226209 |
Durable and efficient gene silencing in vivo by hit-and-run epigenome editing |
| GSE240935 |
Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [targetBSseq_offTargets] |
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| Relations |
| BioSample |
SAMN37000928 |
| SRA |
SRX21380877 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7712395_PBS_2_offTargets.bismark.cov.gz |
8.3 Kb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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